Dr. Shiqi Xu Profile

Dr. Shiqi Xu

at Carl Zeiss X-ray Microscopy Inc

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Author

Publications (9)

Proceedings Article | 19 March 2024 Presentation

Identification of immune cell types based on label-free multiphoton imaging and deep learning

Lucas Kreiss, Amey Chaware, Kanghyun Kim, Kyung Chul Lee, Shiqi Xu, Oana-Maria Thoma, Sarah Lemire, Oliver Friedrich, Sebastian Schürmann, Maximilian Waldner, Roarke Horstmeyer

Proceedings Volume PC12822, PC1282209 (2024) https://doi.org/10.1117/12.3001883

KEYWORDS: Deep learning, Tissues, In vivo imaging, Endoscopy, Education and training, Diseases and disorders, Biopsy, Biological samples, Tissue optics, Neural networks

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Proceedings Article | 13 March 2024 Presentation

Tomographic behavioral tracking of freely-moving model organisms with a hemispheric Fourier light field microscope

Kevin Zhou, Clare Cook, Archan Chakraborty, Joakim Jönsson, Kyung Chul Lee, Xi Yang, Shiqi Xu, Jennifer Bagwell, Donald Fox, Michel Bagnat, Roarke Horstmeyer

Proceedings Volume PC12848, PC128480M (2024) https://doi.org/10.1117/12.3000874

KEYWORDS: Organisms, Microscopes, Tomography, Algorithm development, 3D modeling, Detection and tracking algorithms, 3D tracking, 3D image processing, Reconstruction algorithms, Muscles

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SPIE Journal Paper | 4 March 2024 Open Access

Tensorial tomographic Fourier ptychography with applications to muscle tissue imaging

Shiqi Xu, Xi Yang, Paul Ritter, Xiang Dai, Kyung Chul Lee, Lucas Kreiss, Kevin Zhou, Kanghyun Kim, Amey Chaware, Jadee Neff, Carolyn Glass, Seung Ah Lee, Oliver Friedrich, Roarke Horstmeyer

AP, Vol. 6, Issue 02, 026004, (March 2024) https://doi.org/10.1117/12.10.1117/1.AP.6.2.026004

KEYWORDS: Muscles, Biological samples, Tissues, Tomography, Birefringence, Polarization, Image restoration, Light sources and illumination, Matrices, Biological imaging

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Proceedings Article | 11 August 2023 Presentation + Paper

High-throughput imaging across multiple spatial scales with the multi-camera array microscope (MCAM)

Lucas Kreiss, Kevin Zhou, Kanghyun Kim, Mark Harfouche, Shiqi Xu, Joakim Jönsson, Kyung Chul Lee, Clare Cook, Xi Yang, Paul Reamey, Veton Saliu, Gregor Horstmeyer, Roarke Horstmeyer

Proceedings Volume 12622, 126220S (2023) https://doi.org/10.1117/12.2675451

KEYWORDS: Cameras, Microscopes, Video, Image resolution, 3D image processing, Video microscopy, Stereoscopy, Lens arrays, Imaging systems

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Proceedings Article | 16 March 2023 Presentation

High-throughput tomographic fluorescence imaging with a synchronized camera array (Conference Presentation)

Kevin Zhou, Joakim Jönsson, Clare Cook, Kyung Chul Lee, Xi Yang, Shiqi Xu, Jennifer Bagwell, Archan Chakraborty, Donald Fox, Michel Bagnat, Roarke Horstmeyer

Proceedings Volume PC12390, PC123900C (2023) https://doi.org/10.1117/12.2649458

KEYWORDS: Tomography, Luminescence, Cameras, Organisms, 3D modeling, Objectives, Video, Signal attenuation, Reflectors, Reconstruction algorithms

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SPIE Journal Paper | 30 August 2022 Open Access

Optical imaging and spectroscopy for the study of the human brain: status report

Hasan Ayaz, Wesley Baker, Giles Blaney, David Boas, Heather Bortfeld, Kenneth Brady, Joshua Brake, Sabrina Brigadoi, Erin M. Buckley, Stefan Carp, Robert Cooper, Kyle Cowdrick, Joseph Culver, Ippeita Dan, Hamid Dehghani, Anna Devor, Turgut Durduran, Adam Eggebrecht, Lauren Emberson, Qianqian Fang, Sergio Fantini, Maria Angela Franceschini, Jonas Fischer, Judit Gervain, Joy Hirsch, Keum-Shik Hong, Roarke Horstmeyer, Jana Kainerstorfer, Tiffany Ko, Daniel Licht, Adam Liebert, Robert Luke, Jennifer Lynch, Jaume Mesquida, Rickson Mesquita, Noman Naseer, Sergio Novi, Felipe Orihuela-Espina, Thomas O'Sullivan, Darcy Peterka, Antonio Pifferi, Luca Pollonini, Angelo Sassaroli, João Ricardo Sato, Felix Scholkmann, Lorenzo Spinelli, Vivek Srinivasan, Keith St. Lawrence, Ilias Tachtsidis, Yunjie Tong, Alessandro Torricelli, Tara Urner, Heidrun Wabnitz, Martin Wolf, Ursula Wolf, Shiqi Xu, Changhuei Yang, Arjun Yodh, Meryem Yücel, Wenjun Zhou

NPh, Vol. 9, Issue S2, S24001, (August 2022) https://doi.org/10.1117/12.10.1117/1.NPh.9.S2.S24001

KEYWORDS: Brain, Near infrared spectroscopy, Neuroimaging, Imaging spectroscopy, Sensors, Optical imaging, Optical spectroscopy imaging, Optical spectroscopy, Spectroscopy, Tissue optics

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Proceedings Article | 12 September 2021 Presentation

Imaging anisotropy with vectorial Fourier ptychography

Shiqi Xu, Xiang Dai, Xi Yang, Kevin Zhou, Pavan Konda, Roarke Horstmeyer

Proceedings Volume 11875, 118750F (2021) https://doi.org/10.1117/12.2598999

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Microscopic imaging of anisotropic samples has many important applications in cytopathology. The endogenous contrast from the polarization properties of a specimen, such as its birefringence, provides valuable diagnostic information for several deadly diseases, including cardiac amyloidosis and squamous cell carcinoma, for example. In the past, polarized light microscopy (PLM) has been widely used as a diagnostic tool during the clinical review. However, in analogy with the standard microscope, the PLM typically has a restricted spatial-bandwidth product (SBP). As a consequence, one can either image a large area with low resolution or see the details of a very small area of the sample at the resolutions required for accurate analysis. To address the SBP issue of the PLM, we propose a computational microscopy method, termed vectorial Fourier ptychography, to illuminate the specimen with polarized light from different angles and detects different polarization states of the diffracted light. By illuminating a specimen with plane waves from different angles, our vectorial Fourier ptychography method effectively modulates the high-spatial-frequency components of the specimen into lower frequencies that can be detected by the optical system. With a Jones calculus-based forward model and a second-order phase retrieval method, we can reconstruct high-resolution, wide field-of-view(FOV) amplitude, phase, birefringence, retardance, and diattenuation of the specimen. To assess the reconstruction accuracy of our method, we imaged polystyrene beads submerged in immersion oils of different refractive index, as well as monosodium urate crystals. Further, To validate the diattenuation reconstruction accuracy, we reconstruct a USAF resolution test chart with a half blocked by a linear polarizer. These experiments confirm quantitatively accurate reconstruction results with a 1.25 um full-pitch resolution over a FOV of 6.6 x 4.4 mm^2, which is 5 times higher than the native (brightfield) resolution of the non-computational optical system. Finally, we demonstrate our technique by producing high SBP polarization images of several anisotropic biologic samples, includes collagen tissue, congo red stained cardiac tissue, and a bean root sample.

Proceedings Article | 5 March 2021 Presentation

Imaging decorrelation via deep learning and SPAD array detection

Shiqi Xu, Xi Yang, Wenhui Liu, Ruobing Qian, Pavan Chandra Konda, Roarke Horstmeyer

Proceedings Volume 11629, 116292A (2021) https://doi.org/10.1117/12.2578644

KEYWORDS: Detector arrays, Tissues, Digital micromirror devices, Tissue optics, Temporal resolution, Spectroscopy, Sensors, Scattering media, Natural surfaces, Monte Carlo methods

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Proceedings Article | 5 March 2021 Presentation

Polarization and phase imaging using an LED array microscope

Xiang Dai, Pavan Chandra Konda, Shiqi Xu, Roarke Horstmeyer

Proceedings Volume 11646, 116460U (2021) https://doi.org/10.1117/12.2577344

KEYWORDS: Polarization, Microscopes, Light emitting diodes, Phase imaging, Birefringence, Absorption, Tissues, Spinal cord, Reconstruction algorithms, Polarizers

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Showing 5 of 9 publications

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